Bibliography Report

• PPA Bibliography
• This Report
• Github repository

Introduction

This report assesses the PPA Bibliography in regards to different measures and shows some information of the content. It does not assess the content of the sources but rather the bibliometric data.

Bibliographic analysis

In most cases, the bibliographic analysis is done on the OpenAlex library. In some cases, we can also do it using the Zenodo data. This is mentioned in the beginning of each subsection

Publication types

Analysis: Zenodo and OpenAlex

OpenAlex and Zotero use different tyoes. These are not directly compable, which is whu=y both are shown.

bib_data$figure_types_data |>
  dplyr::arrange(
    from,
    desc(count)
  ) |>
  knitr::kable(
    caption = "Types of documents from the Zotero bibliography as well as from OpenApex."
  )

Types of documents from the Zotero bibliography as well as from OpenApex.

type	count	from
article	833	OpenAlex
review	103	OpenAlex
book-chapter	17	OpenAlex
letter	9	OpenAlex
book	6	OpenAlex
preprint	4	OpenAlex
other	2	OpenAlex
editorial	1	OpenAlex
erratum	1	OpenAlex
journalArticle	1148	Zotero
book	39	Zotero
manuscript	20	Zotero
bookSection	15	Zotero
conferencePaper	9	Zotero
report	4	Zotero
thesis	3	Zotero
artwork	2	Zotero
document	2	Zotero
webpage	2	Zotero

bib_data$figure_types

Zenodo versus OpenAlex Types

Analysis: Zenodo and OpenAlex

The types entered in the Zenodo library and the types as retrieved from OpenAlex are not linked, therefore they can differ. This can indicate faulty data entering in Zenodo but not necessarily has to. These cases need to be carefully evaluated and here only given as a starting point.

NA in OpenAlex is likely caused by the doi not found in OpenAlex (not in there, not valid, non-standard DOI in Zenodo). NA in Zotero is linked to non-standard DOI entries (i.e. with http) which can therefore not be linked to OpenAlex data. If all DOIs are in standard format, there should be no NAs in this Table in the column Ferom Zenodo.

TODO: Improvements should be done after feedback.

bib_data$metrics$types$comparison |>
  knitr::kable(
    col.names = c("Type from Zenodo", "Type from [OpenAlex](https://OpenAlex.org){target='_blank'}", "count"),
    caption = "Table giving the combination of types from Zenodo as well as [OpenAlex](https://OpenAlex.org){target='_blank'} and their frequency"
  )

Table giving the combination of types from Zenodo as well as OpenAlex and their frequency

Type from Zenodo	Type from OpenAlex	count
journalArticle	article	918
journalArticle	NA	207
journalArticle	review	124
book	NA	39
NA	article	30
manuscript	NA	20
journalArticle	book-chapter	16
bookSection	NA	15
journalArticle	letter	9
conferencePaper	NA	6
journalArticle	book	6
report	NA	4
journalArticle	preprint	4
thesis	NA	3
conferencePaper	article	3
webpage	NA	2
journalArticle	other	2
artwork	NA	2
document	NA	2
NA	review	2
journalArticle	erratum	1
journalArticle	editorial	1
NA	book-chapter	1

Year of Publication

Analysis: Zenodo and OpenAlex

The following ranges of publication years can be found in the data.

bib_data$figure_pub_year_data |>
  dplyr::summarize(
    min = min(publication_year, na.rm = TRUE),
    max = max(publication_year, na.rm = TRUE),
    .by = c(from)
  ) |>
  knitr::kable()

from	min	max
Zenodo	1826	2019
OpenAlex	1945	2019

bib_data$figure_pub_year

Warning: Removed 1 row containing missing values or values outside the scale range
(`geom_col()`).

Access Status of References

Analysis: OpenAlex

bib_data$figure_oa_status

50 Most often cited Journals

Analysis: Zenodo

TODO: OpenAlex should be added

bib_data$figure_top_journals

This table contains all Journals as specified in the Zotero database.

bib_data$figure_top_journals_data |>
  IPBES.R::table_dt("cited_journals")

Coutries of Institutes of all authors

Analysis: OpenAlex

In this section we will take a closer look at the countries from which ih the authors ot the publication come. THe data includes all authoirs without weighting.

#|
#| fig-height: 10
#| fig-width: 10

bib_data$figure_top_country_map

This plot only contains the countries with more than 10 references.

#|
#| fig-height: 10
#| fig-width: 10

bib_data$figure_top_country

This table contains all countries and the number of authorship.

bib_data$figure_top_country_data |>
  IPBES.R::table_dt("top_countries")

Cleanliness of the Bibliography

Cleanliness of a bibliography is defined here as the quality of the bibliografic data in the bibliography. It does not concern any topical measures, only measures related to the bibliografic data in the bibliography.

The analysis is at the moment only done for DOIs as corresponding measures are not available at the moment for ISBNs and ISSNs and duplicate ISBNs and ISSNs can be rcorrect as different chapters of a book might be in the bibliography.

Entries with DOIs, ISBNs or ISSNs in Zotero

To identify a reference, the most widely used identifier is the DOI. The following table shows the number of references with a DOI and the number of unique DOIs.

To consider duplicate ISBNs or ISSNs as duplicates entries in the library is not waranted as e.g. differenc chapters of a book can be separate entries in the library and therefore lead to duplicates.

• DOIs: 996 (80.06%) - 138 duplicates
• ISBNss: 16 (1.29%)
• ISBNss: 953 (76.61%)

DOIs in Zotero

The following sections provide some more detailed analysis of the bibliography in Zenodo. The tables all contain clickable links which, shwen clicked, show the respective article in the Zotero bibliograpohy.

Duplicates

The following DOIs are duplicates in the bibliography. This table should be empty.

if (length(bib_data$metrics$zotero_dois$duplicate) > 0) {
  data.frame(
    doi = bib_data$metrics$zotero_dois$duplicate,
    link = paste0(bib_data$bibliography$url, "/items/", names(bib_data$metrics$zotero_dois$duplicate))
  ) |>
    dplyr::mutate(
      sort = doi,
      doi = paste0('<a href="', link, '" target="_blank">', doi, "</a>"),
    ) |>
    dplyr::arrange(
      sort
    ) |>
    dplyr::mutate(
      sort = NULL
    ) |>
    knitr::kable(
      caption = "DOIs in Zenodo which are duplicated",
      escape = FALSE
    )
}

DOIs in Zenodo which are duplicated

	doi	link
WVEZYS8X	10.1007/s10144-006-0010-8	https://www.zotero.org/groups/2333088/items/WVEZYS8X
A9ABHH3Y	10.1007/s10144-006-0010-8	https://www.zotero.org/groups/2333088/items/A9ABHH3Y
38EBH2KQ	10.1007/s13592-014-0316-z	https://www.zotero.org/groups/2333088/items/38EBH2KQ
XHAHZY9B	10.1007/s13592-014-0316-z	https://www.zotero.org/groups/2333088/items/XHAHZY9B
Z6DIJXQQ	10.1016/j.baae.2010.01.001	https://www.zotero.org/groups/2333088/items/Z6DIJXQQ
4JZ6YT5C	10.1016/j.baae.2010.01.001	https://www.zotero.org/groups/2333088/items/4JZ6YT5C
PHR83VI7	10.1016/j.biocon.2005.11.013	https://www.zotero.org/groups/2333088/items/PHR83VI7
M63PKPKL	10.1016/j.biocon.2005.11.013	https://www.zotero.org/groups/2333088/items/M63PKPKL
IDJ4TIFH	10.1016/j.biocon.2006.07.023	https://www.zotero.org/groups/2333088/items/IDJ4TIFH
H99N6JRC	10.1016/j.biocon.2006.07.023	https://www.zotero.org/groups/2333088/items/H99N6JRC
4XQ6JBI4	10.1016/j.biocon.2012.10.021	https://www.zotero.org/groups/2333088/items/4XQ6JBI4
5N62E4A5	10.1016/j.biocon.2012.10.021	https://www.zotero.org/groups/2333088/items/5N62E4A5
9QG7M9YI	10.1016/j.cub.2008.08.066	https://www.zotero.org/groups/2333088/items/9QG7M9YI
LRWFAQWP	10.1016/j.cub.2008.08.066	https://www.zotero.org/groups/2333088/items/LRWFAQWP
W6KIHF72	10.1016/j.ecolecon.2008.06.014	https://www.zotero.org/groups/2333088/items/W6KIHF72
JLR5VCU9	10.1016/j.ecolecon.2008.06.014	https://www.zotero.org/groups/2333088/items/JLR5VCU9
DN836Z7G	10.1016/j.ppees.2010.02.005	https://www.zotero.org/groups/2333088/items/DN836Z7G
RCQ3U4NU	10.1016/j.ppees.2010.02.005	https://www.zotero.org/groups/2333088/items/RCQ3U4NU
A794T4ZN	10.1016/j.tree.2010.01.007	https://www.zotero.org/groups/2333088/items/A794T4ZN
M8EZ855N	10.1016/j.tree.2010.01.007	https://www.zotero.org/groups/2333088/items/M8EZ855N
3CHHG326	10.1016/j.tree.2013.05.008	https://www.zotero.org/groups/2333088/items/3CHHG326
RSXKWZBA	10.1016/j.tree.2013.05.008	https://www.zotero.org/groups/2333088/items/RSXKWZBA
2J9IIF8D	10.1017/s0889189300003179	https://www.zotero.org/groups/2333088/items/2J9IIF8D
2Y3BE2H7	10.1017/s0889189300003179	https://www.zotero.org/groups/2333088/items/2Y3BE2H7
VJMDYZ54	10.1038/nature10452	https://www.zotero.org/groups/2333088/items/VJMDYZ54
2WKR9TBQ	10.1038/nature10452	https://www.zotero.org/groups/2333088/items/2WKR9TBQ
QVZC647I	10.1046/j.1472-4642.2002.00148.x	https://www.zotero.org/groups/2333088/items/QVZC647I
B9IWS8QU	10.1046/j.1472-4642.2002.00148.x	https://www.zotero.org/groups/2333088/items/B9IWS8QU
2K57HPB7	10.1051/apido:2006027	https://www.zotero.org/groups/2333088/items/2K57HPB7
73W6G85C	10.1051/apido:2006027	https://www.zotero.org/groups/2333088/items/73W6G85C
AJUTZI4U	10.1073/pnas.1012431108	https://www.zotero.org/groups/2333088/items/AJUTZI4U
NXGWLKTW	10.1073/pnas.1012431108	https://www.zotero.org/groups/2333088/items/NXGWLKTW
UKC6IMQB	10.1073/pnas.1115559108	https://www.zotero.org/groups/2333088/items/UKC6IMQB
JRXWV2XQ	10.1073/pnas.1115559108	https://www.zotero.org/groups/2333088/items/JRXWV2XQ
8YGU2AIA	10.1073/pnas.1218503110	https://www.zotero.org/groups/2333088/items/8YGU2AIA
YBSZQBBW	10.1073/pnas.1218503110	https://www.zotero.org/groups/2333088/items/YBSZQBBW
V5XLA8TI	10.1073/pnas.1218503110	https://www.zotero.org/groups/2333088/items/V5XLA8TI
CJ784JEY	10.1073/pnas.1307438110	https://www.zotero.org/groups/2333088/items/CJ784JEY
YTXYUNRE	10.1073/pnas.1307438110	https://www.zotero.org/groups/2333088/items/YTXYUNRE
K5H2FYID	10.1073/pnas.1323073111	https://www.zotero.org/groups/2333088/items/K5H2FYID
XTPX6FMJ	10.1073/pnas.1323073111	https://www.zotero.org/groups/2333088/items/XTPX6FMJ
J5SSG6NE	10.1073/pnas.262413599	https://www.zotero.org/groups/2333088/items/J5SSG6NE
78WTYNH2	10.1073/pnas.262413599	https://www.zotero.org/groups/2333088/items/78WTYNH2
W3HLZB8H	10.1079/ijt20048	https://www.zotero.org/groups/2333088/items/W3HLZB8H
KV4YCKSC	10.1079/ijt20048	https://www.zotero.org/groups/2333088/items/KV4YCKSC
VA4DBX4Z	10.1080/0005772x.2001.11099523	https://www.zotero.org/groups/2333088/items/VA4DBX4Z
76HJABBG	10.1080/0005772x.2001.11099523	https://www.zotero.org/groups/2333088/items/76HJABBG
VADN6LUQ	10.1098/rspb.2004.2909	https://www.zotero.org/groups/2333088/items/VADN6LUQ
UDN9MUSE	10.1098/rspb.2004.2909	https://www.zotero.org/groups/2333088/items/UDN9MUSE
CJB52BPU	10.1098/rspb.2004.2909	https://www.zotero.org/groups/2333088/items/CJB52BPU
EC6RU4TS	10.1098/rspb.2006.3721	https://www.zotero.org/groups/2333088/items/EC6RU4TS
MBLLD8Q2	10.1098/rspb.2006.3721	https://www.zotero.org/groups/2333088/items/MBLLD8Q2
7VJLICRV	10.1098/rspb.2008.0405	https://www.zotero.org/groups/2333088/items/7VJLICRV
TC6WN7LB	10.1098/rspb.2008.0405	https://www.zotero.org/groups/2333088/items/TC6WN7LB
7XV4RZW9	10.1098/rspb.2014.1358	https://www.zotero.org/groups/2333088/items/7XV4RZW9
CUPQHECF	10.1098/rspb.2014.1358	https://www.zotero.org/groups/2333088/items/CUPQHECF
MBY6ZYTM	10.1098/rspb.2014.1799	https://www.zotero.org/groups/2333088/items/MBY6ZYTM
EGQXLPE3	10.1098/rspb.2014.1799	https://www.zotero.org/groups/2333088/items/EGQXLPE3
8BB6H83X	10.1111/1365-2664.12385	https://www.zotero.org/groups/2333088/items/8BB6H83X
T26DEHXP	10.1111/1365-2664.12385	https://www.zotero.org/groups/2333088/items/T26DEHXP
KH845RKT	10.1111/ele.12121	https://www.zotero.org/groups/2333088/items/KH845RKT
WKZNSBE4	10.1111/ele.12121	https://www.zotero.org/groups/2333088/items/WKZNSBE4
SKMTCSGM	10.1111/ele.12325	https://www.zotero.org/groups/2333088/items/SKMTCSGM
74FW2LX5	10.1111/ele.12325	https://www.zotero.org/groups/2333088/items/74FW2LX5
PYDXHHJI	10.1111/j.1365-2311.2010.01234.x	https://www.zotero.org/groups/2333088/items/PYDXHHJI
2N3GV7J6	10.1111/j.1365-2311.2010.01234.x	https://www.zotero.org/groups/2333088/items/2N3GV7J6
S5GHCK3W	10.1111/j.1365-2745.2012.01968.x	https://www.zotero.org/groups/2333088/items/S5GHCK3W
XKEWCXCA	10.1111/j.1365-2745.2012.01968.x	https://www.zotero.org/groups/2333088/items/XKEWCXCA
487K4XHR	10.1111/j.1442-9993.2004.01376.x	https://www.zotero.org/groups/2333088/items/487K4XHR
A9PZJ8NA	10.1111/j.1442-9993.2004.01376.x	https://www.zotero.org/groups/2333088/items/A9PZJ8NA
WWFBQD22	10.1111/j.1461-0248.2007.01018.x	https://www.zotero.org/groups/2333088/items/WWFBQD22
KG6HJFC4	10.1111/j.1461-0248.2007.01018.x	https://www.zotero.org/groups/2333088/items/KG6HJFC4
PJ72USDB	10.1111/j.1461-0248.2007.01061.x	https://www.zotero.org/groups/2333088/items/PJ72USDB
6ILXDY58	10.1111/j.1461-0248.2007.01061.x	https://www.zotero.org/groups/2333088/items/6ILXDY58
N4PUS2A4	10.1111/j.1461-0248.2008.01170.x	https://www.zotero.org/groups/2333088/items/N4PUS2A4
89T8XZU3	10.1111/j.1461-0248.2008.01170.x	https://www.zotero.org/groups/2333088/items/89T8XZU3
3JS5ATGE	10.1111/j.1461-0248.2008.01269.x	https://www.zotero.org/groups/2333088/items/3JS5ATGE
NUTV32N4	10.1111/j.1461-0248.2008.01269.x	https://www.zotero.org/groups/2333088/items/NUTV32N4
EPSUJ937	10.1111/j.1461-0248.2010.01579.x	https://www.zotero.org/groups/2333088/items/EPSUJ937
IXNBR5FB	10.1111/j.1461-0248.2010.01579.x	https://www.zotero.org/groups/2333088/items/IXNBR5FB
AXIN7HHU	10.1111/j.1461-0248.2011.01669.x	https://www.zotero.org/groups/2333088/items/AXIN7HHU
65XTVC8N	10.1111/j.1461-0248.2011.01669.x	https://www.zotero.org/groups/2333088/items/65XTVC8N
AXKFB2KK	10.1111/j.1469-185x.2011.00216.x	https://www.zotero.org/groups/2333088/items/AXKFB2KK
SBUW532J	10.1111/j.1469-185x.2011.00216.x	https://www.zotero.org/groups/2333088/items/SBUW532J
FTHPMCYA	10.1111/j.1523-1739.2009.01331.x	https://www.zotero.org/groups/2333088/items/FTHPMCYA
BPMF6BST	10.1111/j.1523-1739.2009.01331.x	https://www.zotero.org/groups/2333088/items/BPMF6BST
CX3WXJIV	10.1111/j.1600-0706.2010.18644.x	https://www.zotero.org/groups/2333088/items/CX3WXJIV
852V2M3B	10.1111/j.1600-0706.2010.18644.x	https://www.zotero.org/groups/2333088/items/852V2M3B
A6IPNURS	10.1111/j.1600-0706.2013.00644.x	https://www.zotero.org/groups/2333088/items/A6IPNURS
2F4PUAJD	10.1111/j.1600-0706.2013.00644.x	https://www.zotero.org/groups/2333088/items/2F4PUAJD
M3GPRR8W	10.1126/science.1127863	https://www.zotero.org/groups/2333088/items/M3GPRR8W
54KP8VYA	10.1126/science.1127863	https://www.zotero.org/groups/2333088/items/54KP8VYA
RD3Z7D4T	10.1126/science.1185383	https://www.zotero.org/groups/2333088/items/RD3Z7D4T
5L22ZQ5J	10.1126/science.1185383	https://www.zotero.org/groups/2333088/items/5L22ZQ5J
BC6ETLLH	10.1126/science.1230200	https://www.zotero.org/groups/2333088/items/BC6ETLLH
2A5IMXME	10.1126/science.1230200	https://www.zotero.org/groups/2333088/items/2A5IMXME
DAYK5U2W	10.1126/science.1257259	https://www.zotero.org/groups/2333088/items/DAYK5U2W
ZS5I23CD	10.1126/science.1257259	https://www.zotero.org/groups/2333088/items/ZS5I23CD
NQP27N4D	10.1126/science.aaa7031	https://www.zotero.org/groups/2333088/items/NQP27N4D
3HW29STE	10.1126/science.aaa7031	https://www.zotero.org/groups/2333088/items/3HW29STE
NC3I88VP	10.1146/annurev-ecolsys-102710-145042	https://www.zotero.org/groups/2333088/items/NC3I88VP
HHVPM8K6	10.1146/annurev-ecolsys-102710-145042	https://www.zotero.org/groups/2333088/items/HHVPM8K6
V6VGJURY	10.1146/annurev.ecolsys.29.1.83	https://www.zotero.org/groups/2333088/items/V6VGJURY
6LQS4LHQ	10.1146/annurev.ecolsys.29.1.83	https://www.zotero.org/groups/2333088/items/6LQS4LHQ
2RK256GT	10.1146/annurev.ecolsys.34.011802.132355	https://www.zotero.org/groups/2333088/items/2RK256GT
V8WVP533	10.1146/annurev.ecolsys.34.011802.132355	https://www.zotero.org/groups/2333088/items/V8WVP533
9RM2B8D7	10.1146/annurev.ecolsys.38.091206.095818	https://www.zotero.org/groups/2333088/items/9RM2B8D7
JIW52VJB	10.1146/annurev.ecolsys.38.091206.095818	https://www.zotero.org/groups/2333088/items/JIW52VJB
8ZL2RP6M	10.1146/annurev.en.22.010177.001141	https://www.zotero.org/groups/2333088/items/8ZL2RP6M
GA4BP7DE	10.1146/annurev.en.22.010177.001141	https://www.zotero.org/groups/2333088/items/GA4BP7DE
GEXNIG3M	10.1146/annurev.en.28.010183.002203	https://www.zotero.org/groups/2333088/items/GEXNIG3M
AGAC3VGB	10.1146/annurev.en.28.010183.002203	https://www.zotero.org/groups/2333088/items/AGAC3VGB
3JVCKVKM	10.1371/journal.pone.0002771	https://www.zotero.org/groups/2333088/items/3JVCKVKM
DKY9V3U4	10.1371/journal.pone.0002771	https://www.zotero.org/groups/2333088/items/DKY9V3U4
H5SSBJ33	10.1371/journal.pone.0021363	https://www.zotero.org/groups/2333088/items/H5SSBJ33
XHQ4G677	10.1371/journal.pone.0021363	https://www.zotero.org/groups/2333088/items/XHQ4G677
ASJV5ZLZ	10.1371/journal.pone.0030641	https://www.zotero.org/groups/2333088/items/ASJV5ZLZ
IEQS39YC	10.1371/journal.pone.0030641	https://www.zotero.org/groups/2333088/items/IEQS39YC
4N387LWY	10.1371/journal.pone.0035954	https://www.zotero.org/groups/2333088/items/4N387LWY
DIP25RQF	10.1371/journal.pone.0035954	https://www.zotero.org/groups/2333088/items/DIP25RQF
FUL2L98W	10.1890/03-5271	https://www.zotero.org/groups/2333088/items/FUL2L98W
LJS2FJXG	10.1890/03-5271	https://www.zotero.org/groups/2333088/items/LJS2FJXG
G6CZD6Q2	10.1890/120321	https://www.zotero.org/groups/2333088/items/G6CZD6Q2
TATH842X	10.1890/120321	https://www.zotero.org/groups/2333088/items/TATH842X
ZEU2XBPM	10.1890/130330	https://www.zotero.org/groups/2333088/items/ZEU2XBPM
2LRFV22A	10.1890/130330	https://www.zotero.org/groups/2333088/items/2LRFV22A
U2964AG7	10.2307/3071954	https://www.zotero.org/groups/2333088/items/U2964AG7
T8ZV4T73	10.2307/3071954	https://www.zotero.org/groups/2333088/items/T8ZV4T73
ITAQ34S8	10.26786/1920-7603(2014)1	https://www.zotero.org/groups/2333088/items/ITAQ34S8
QFP5VB5K	10.26786/1920-7603(2014)1	https://www.zotero.org/groups/2333088/items/QFP5VB5K
UMHMCQ9W	10.2980/i1195-6860-12-3-289.1	https://www.zotero.org/groups/2333088/items/UMHMCQ9W
UFHNS4JV	10.2980/i1195-6860-12-3-289.1	https://www.zotero.org/groups/2333088/items/UFHNS4JV
UDB72QZB	10.3896/ibra.1.50.1.02	https://www.zotero.org/groups/2333088/items/UDB72QZB
XKNBJCNV	10.3896/ibra.1.50.1.02	https://www.zotero.org/groups/2333088/items/XKNBJCNV
QVTBMMLC	10.3896/ibra.1.52.4.12	https://www.zotero.org/groups/2333088/items/QVTBMMLC
BALEB3R9	10.3896/ibra.1.52.4.12	https://www.zotero.org/groups/2333088/items/BALEB3R9
RLDIUJNW	10.4039/ent133439-4	https://www.zotero.org/groups/2333088/items/RLDIUJNW
QYNAZTSA	10.4039/ent133439-4	https://www.zotero.org/groups/2333088/items/QYNAZTSA

Non Standard

All DOIs should be given as only the DOI without the resolver, i.e. not starting with http. The following table shows all entries which do have a non-conform DOI:

#|

http <- grep("http", bib_data$metrics$zotero_dois$id_raw)
data.frame(
  doi = bib_data$metrics$zotero_dois$id_raw[http],
  link = paste0(bib_data$bibliography$url, "/items/", names(bib_data$metrics$zotero_dois$id_raw)[http])
) |>
  dplyr::mutate(
    doi = paste0('<a href="', link, '" target="_blank">', doi, "</a>"),
    link = NULL
  ) |>
  knitr::kable(
    caption = "DOIs in Zenodo which include a `http`",
    escape = FALSE
  )

DOIs in Zenodo which include a http

	doi
HS3NDPZ8	https://doi.org/10.1890/1540-9295(2007)5[80:SHIUER]2.0.CO;2
4ZI4KS98	http://dx.doi.org/10.5751/
NQSUD2SH	http://dx.doi.org/10.1371/journal.pone.0094459

Not Valid

Here we do acheck for the structural validity of the dois. This check needs to be improved. Of these 52 are not valid. These are:

#|

if (length(bib_data$metrics$zotero_dois$not_valid) > 0) {
  data.frame(
    doi = bib_data$metrics$zotero_dois$not_valid,
    link = paste0(bib_data$bibliography$url, "/items/", names(bib_data$metrics$zotero_dois$not_valid))
  ) |>
    dplyr::mutate(
      doi = paste0('<a href="', link, '" target="_blank">', doi, "</a>"),
      link = NULL
    ) |>
    knitr::kable(
      caption = "DOIs in Zenodo which ar not valid",
      escape = FALSE
    )
} else {
  print("All DOIs in Zenodo are valid.")
}

DOIs in Zenodo which ar not valid

	doi
Y5NSPPUH	e0118748
ALGHGTVC	10. 1111/1462-2920.12426
UTY8BT2Z	10.1641/0006-3568(2001)051[0625:RHOREM]2.0.CO;2
NCX3RHJN	e111629
HS3NDPZ8	10.1890/1540-9295(2007)5[80:SHIUER]2.0.CO;2
4ZI4KS98	10.5751/
I3LT26P2	10.2984/1534-6188(2007)61[173:csoteb]2.0.co;2
QA7ES7M2	10.1603/0013-8746(2000)093[0415:mdriae]2.0.co;2
AYNKG7GY	e1004816
UH9IEFBP	10.1674/0003-0031(2007)157[92:ropact]2.0.co;2
P244RZKW	10.1603/0013-8746(2001)094[0545:sypfot]2.0.co;2
PYY5358N	10.1603/0013-8746(2002)095[0345:cpeabh]2.0.co;2
8FC7HMHK	10.1890/1051-0761(2000)010[0689:BICEGC]2.0.CO;2

Not in OpenAlex

To validate the existence and validity of the DOIs, we check if the DOIs are in the OpenAlex database.

Of the 996 unique DOIs in the library, 52 (5.22%) are in not in OpenAlex. This includes the non-valid DOIS, which are filtered out in the table below.

data.frame(
  doi = bib_data$metrics$zotero_dois$not_in_oa,
  link = paste0(bib_data$bibliography$url, "/items/", names(bib_data$metrics$zotero_dois$not_in_oa))
) |>
  dplyr::mutate(
    doi = paste0('<a href="', link, '" target="_blank">', doi, "</a>"),
    link = NULL
  ) |>
  knitr::kable(
    caption = "DOIs in Zenodo which ar not in [OpenAlex](https://OpenAlex.org){target='_blank'}",
    escape = FALSE
  )

DOIs in Zenodo which ar not in OpenAlex

	doi
WFIZ8XS3	10.1007/BF00115313
53ATEI2G	10.1111/j.1365-294X.2006.02797.x
VVXJVXTC	10.1111/j.1365-294X.2010.04868.x
QUIAB4VC	10.3965/j.issn.1934-6344.2010.01.001-025
Y5NSPPUH	e0118748
ALGHGTVC	10. 1111/1462-2920.12426
JGWG9J99	10.1111/j.1526-100X.2005.00061.x
JI4D77RA	10.1016/S0932-4739(96)80059-9
UTY8BT2Z	10.1641/0006-3568(2001)051[0625:RHOREM]2.0.CO;2
NCX3RHJN	e111629
3F2TA86S	10.1371/Citation
9S7JVVPV	10.1128/AEM.67.5.2384-2387.2001
6IQGI2EY	10.1029/2007GB002947
9PCAHWCL	10.1023/A:1011371119290
LJITKCHV	10.1017/S0021859605005708
8MFQ3Z6R	10.1080/0005772X.1991.11099088
HS3NDPZ8	10.1890/1540-9295(2007)5[80:SHIUER]2.0.CO;2
KITA63RH	10.1097/01.ACM.0000426356.35520.8c
MUL6X3AQ	10.1023/A:1010719107006
BYJ8KZ8S	10.1002/ps.3290
KJN4HKCG	10.1890/ES12-00118.1
KRUFMNNX	10.5435/JAAOS-D-16-00646
97G5KICY	10.1111/j.1654-109X.2010.01098.x
4ZI4KS98	10.5751/
NE64KTWD	10.5751/ES-05035-170440
NQI9JI6I	10.1016/0167-8809(92)90087-R
J2C3RL9B	10.1128/mBio.00898-13
IMZPNPMY	10.1080/0005772X.1995.11099259
I3LT26P2	10.2984/1534-6188(2007)61[173:csoteb]2.0.co;2
QA7ES7M2	10.1603/0013-8746(2000)093[0415:mdriae]2.0.co;2
AYNKG7GY	e1004816
RNCEEFLD	10.1016/S0076-6879(94)33028-X
NQSUD2SH	10.1371/journal.pone.0094459
UVHYPCNR	10.1007/S004420100803
VL46YDRX	10.1111/j.1469-185X.2011.00205.x
W4CARF3Q	10.1016/B978-0-12-396992-7.00002-2
WIS384DH	10.3896/IBRA.1.52.2.01
UH9IEFBP	10.1674/0003-0031(2007)157[92:ropact]2.0.co;2
CHJQP3V9	10.1080/0005772X.2000.11099481
5Q9RYXGI	10.1111/j.1365-294X.2007.03226.x
XEYP6SXP	10.1128/AEM.02227-09
YKPZXXGA	10.1007/BF00704877
TECNNC63	10.1080/0005772X.2004.11099624
GMYRYEKQ	10.1130/GSAT151A.1
MXUXAFMA	10.1007/BF00177048
P244RZKW	10.1603/0013-8746(2001)094[0545:sypfot]2.0.co;2
KQHBRFKS	10.1007/BF00226208
PYY5358N	10.1603/0013-8746(2002)095[0345:cpeabh]2.0.co;2
MWGG8XH5	10.3896/IBRA.1.52.2.18
P7L75H8Q	10.1111/j.1755-263X.2010.00097.x
VNB7C7I9	10.1641/B570306
8FC7HMHK	10.1890/1051-0761(2000)010[0689:BICEGC]2.0.CO;2

TODO Do Exist

TODO Finally we check, if these dois exist but are not ingested into OpenAlex. This is done using the doi.org resolver This is disabled at the moment and still needs to be implemented.